Knut Rudi

Benchmarking 16S rRNA gene amplicon analysis in high-diversity microbial communities reveals fundamental trade-offs in clustering and denoising

This study benchmarks 16S rRNA gene analysis pipelines in high-diversity datasets, revealing trade-offs between clustering accuracy, species recovery, and abundance reconstruction.

Rsearch: An R interface to VSEARCH supporting visualization and parameter tuning

Rsearch runs VSEARCH from R with quality plots, trimming optimizers and phyloseq conversion; on a 16S mock community it matched DADA2's abundance accuracy with fewer, more prevalent OTUs.

A Targeted Reference Database for Improved Analysis of Environmental 16S rRNA Oxford Nanopore Sequencing Data

The paper develops a targeted reference database, AQUAeD-DB, to improve taxonomic accuracy of 16S rRNA sequencing data from seafloor sediments using Oxford Nanopore Technologies.

Enhanced Prediction of Seafloor Ecological State Using 16S Nanopore Sequencing

This study compares Illumina and Nanopore 16S rRNA sequencing for predicting seafloor ecological state using machine learning and feature selection, showing comparable performance with Nanopore as a viable alternative.

Key roles of microbial sulfur and ammonium oxidizers for the coastal seafloor ecological state

The paper examines the relationship between microbial sulfur and ammonium oxidizers and macrofaunal state in coastal seafloor samples, finding distinct microbial networks linked to macrofauna loss or preservation.

Tracing of streptococcal strains from infant stool across human body sites links gut specificity to adhesins

The paper traces streptococcal strains from infant stool to other body sites, showing gut-specific strains are linked to adhesin gene differences.

The effect of dietary chitin on Atlantic salmon (Salmo salar) chitinase activity, gene expression, and microbial composition

This study examines how dietary chitin affects chitinase activity, gene expression, and gut microbial composition in Atlantic salmon.

Association of gut microbiota with metabolism in juvenile Atlantic Salmon

This study examines the relationship between gut microbiota and metabolism in Atlantic salmon, finding significant associations between specific microbial OTUs and metabolic phenotypes.

Genetic diversity and mother-child overlap of the gut associated microbiota determined by reduced genome sequencing

The paper uses reduced metagenome sequencing to analyze genetic diversity and mother-child sharing of gut microbiota in 17 pairs, finding significant sequence overlap and transmission of specific bacteria.